Mercurial > repos > iuc > mothur_phylotype
diff phylotype.xml @ 3:61846dca0ad1 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 09:14:14 -0500 |
| parents | 4f5ecd0c94b3 |
| children | a9da762b1688 |
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--- a/phylotype.xml Tue Sep 05 16:39:10 2017 -0400 +++ b/phylotype.xml Wed Feb 14 09:14:14 2018 -0500 @@ -7,27 +7,27 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$taxonomy" taxonomy.dat && - ln -s "$name" name.dat && +## create symlinks to input datasets +ln -s '$taxonomy' taxonomy.dat && +ln -s '$name' name.dat && - echo 'phylotype( - taxonomy=taxonomy.dat - #if $cutoff: - ,cutoff=$cutoff - #end if - #if $name: - ,name=name.dat - #end if - #if $label: - ,label=${ str($label).replace(",","-") } - #end if - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'phylotype( + taxonomy=taxonomy.dat + #if $cutoff: + ,cutoff=$cutoff + #end if + #if $name: + ,name=name.dat + #end if + #if $label: + ,label=${ str($label).replace(",","-") } + #end if +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy"/> @@ -71,8 +71,7 @@ <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -85,7 +84,6 @@ .. _sabund: https://www.mothur.org/wiki/Sabund_file .. _phylotype: https://www.mothur.org/wiki/Phylotype -]]> - </help> + ]]></help> <expand macro="citations"/> </tool>